QIIME/en: Difference between revisions

'''QIIME''' (pronounced ''chime'') stands for ''Quantitative Insights Into [https://en.wikipedia.org/wiki/Microbial_ecology Microbial Ecology]'', is an open-source [https://en.wikipedia.org/wiki/Bioinformatics bioinformatics] pipeline for performing [https://en.wikipedia.org/wiki/Microbiota microbiome] analysis from raw DNA sequencing data. QIIME is designed to take users from raw sequencing data generated on [https://www.illumina.com/ Illumina] or other platforms to publication-quality graphics and statistics. This includes demultiplexing and quality filtering, [https://en.wikipedia.org/wiki/Operational_taxonomic_unit OTU] picking, taxonomic assignment, phylogenetic reconstruction, diversity analyses and visualizations. QIIME has been applied to studies based on billions of sequences from tens of thousands of samples.

'''Note''': QIIME 2 has replaced QIIME 1 as of January 1, 2018; version 1 is no longer supported.

'''Note''': As of February, 2020, due to various issues generated by Conda environments in our HPC systems, '''installation using Anaconda or Miniconda is no longer supported'''.

QIIME2 can be installed using [[Apptainer]] or using EasyBuild. Apptainer is strongly preferred since it does not generate many thousands of files in your home directory, potentially causing you to exceed the disk quota limit on the number of files.

The QIIME2 developers publish images on [https://quay.io/organization/qiime2 Quay.io].  In order to use one of these images on our systems you must first build an Apptainer image:

Note that it is important to use the [[Apptainer#Bind_mounts|bind]] option (<tt>-B</tt>) with each folder you want to work with when you run programs in your container. For more information about Apptainer, you can watch the recorded [https://www.youtube.com/watch?v=bpmrfVqBowY Apptainer webinar].

On first importing data into QIIME format you may receive an error ending with a message like this:

[http://qiime.org/ QIIME homepage]<br>